/* 
 * Author: Chih-Chiang Tsou <chihchiang.tsou@gmail.com>
 *             Nesvizhskii Lab, Department of Computational Medicine and Bioinformatics, 
 *             University of Michigan, Ann Arbor
 *
 * Copyright 2014 University of Michigan, Ann Arbor, MI
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package MSUmpire.SpectraST;

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.io.FilenameUtils;

/**
 *
 * @author Chih-Chiang Tsou <chihchiang.tsou@gmail.com>
 */
public class SpectraSTCreateLib {

    public void CreateLib(String pepxml) throws IOException, InterruptedException {

        String[] msconvertcmd = {"spectrast", "-cP0.9", "-cN" + FilenameUtils.getBaseName(pepxml) + "splib", pepxml};
        Process p = Runtime.getRuntime().exec(msconvertcmd);
        System.out.print("constructing spectralib...." + pepxml + "\n");
        p.waitFor();
        PrintOutput(p);
    }

    private void PrintOutput(Process p) throws IOException {
        BufferedReader is;  // reader for output of process
        String line;
        is = new BufferedReader(new InputStreamReader(p.getInputStream()));
        while ((line = is.readLine()) != null) {
            if (!"".equals(line.trim())) {
                System.out.println(line);
            }
        }
    }
}
